Comparative Genomics of the Human Oral Spirochetes Treponema denticola and T. putidum

Abstract

Background More than 75 species/species-level phylotypes of spirochetes belonging to the genus Treponema inhabit the human oral cavity. The phylogroup 2 species T. denticola is associated to periodontitis, a common oral inflammation disease. T. putidum is a closely related species isolated from human periodontitis lesion but its clinical relevance and physiology being largely unknown. We have sequenced the whole genome of 4 human oral T. putidum isolates and compared them with 17 human T. denticola strains. Methods T. putidum strains (supplied by Dr. Chris Wyss) were cultured anaerobically in TYGVS medium and their genomic DNA was purified (Promega, Wizard genomic DNA purification kit). Whole genomes were sequenced using both the Oxford Nanopore Technology MinION (R9.4) and Illumina Hi-Seq (PE150) platforms. Hybrid de novo assembly was performed using canu and pilon. The complete genome was annotated using prokka and compared using roary and KEGG database. Results The average genome size for the human oral T. putidum strains was 2.86 Mbp, with a GC content of 37.24%. There were ca. 2,700 predicted coding sequences (CDs) in each strain. Two sets of the 16S-23S-5S rRNA operon were observed in all treponeme genomes. We detected the tRNA-Gly-CCC in all 4 T. putidum strains but not in any T. denticola strain (n = 17). The average nucleotide identities (ANI) within the T. putidum genomes (n = 4) was 98.4%. ANI between T. putidum and T. denticola strains was 88.3%. Pen-genome analysis of these 21 oral treponeme genomes revealed a core gene set of 602 genes. T. putidum and T. denticola species carried 2,324 and 4,837 specific genes, respectively. They shared 1,369 genes (16% of pen-genome size) in common. Prophage regions were predicted in all T. putidum strains. The lack of dentilisin and sialidase genes in the T. putidum genomes is consistent with their reported phenotypic characteristics. T. putidum possess unique sets of genes absent in T. denticola species such as the altronate dehydratase (EC:4.2.1.7) and 2-keto-3-deoxygluconate permease (K02526) involved in D-Galacturonate degradation and proton sympoter activity, respectively. Conclusions Treponema putidum species has a single genome whose size and composition share many similarities with those of T. denticola strains characterized to date. However, it has distinct genomic and phenotypic features suggesting niche differentiation from T. denticola.